Hi,
I'm a new modeller user trying to model some closely related proteins for docking purposes. I would like to model the binding site of the ligand as well as possible. The template file I'm using has the ligand in the binding site. I would like to know is there an easy way of setting the restraints for the most important residues? Should I use the MAKE_RESTRAINTS command somehow or is it more reliable to use another program like Sybyl or Insight to choose the restraints? Also the command SET HETATM_IO allways gives me an error:
Number of residues in the alignment and pdb files are different: 280 282 Might this be related to the fact that there are two phosphorylated residues in the template?
I would love to see a more thorough tutorial on modelling using restraints.
[Aki]
Aki Heikkilä Department of pharmaceutical chemistry University of Helsinki